I set up my Visual Studio Team Service account to clone my private GitHub repo and build the Windows UWP application anytime I queue a build. The cloning works without any issue
I too was getting the error:
"Cannot import the key file 'blah.pfx'. The key file may be password protected. To correct this, try to import the certificate manually into the current user’s personal certificate store".
You can double click a .pfx file to import it into your store, the trick is that when it brings up the wizard, you have to choose "Current User", instead of "Local Machine" on the first screen, then instead of "Automatic", I specifically chose "Personal".
I was able to build the package after that. Didn't work when I chose "Local Machine" + Personal.